[Bioc-devel] Fwd: BiocInstaller::useDevel() Error: 'devel' version requires a more recent R

Hi again,

I applied your YAML config in my latest commit
<https://github.com/kevinrue/TVTB/blob/master/.travis.yml>
But in my (ongoing) Travis build
<https://travis-ci.org/kevinrue/TVTB/builds/169301723>, I can already see
that it has installed the wrong R version (3.1.1, not devel), see line 370
<https://travis-ci.org/kevinrue/TVTB/builds/169301723#L370>

$ curl -Lo /tmp/R-3.3.1.xz https://s3.amazonaws.com/
rstudio-travis/R-3.3.1.xz

As opposed to the configuration I posted earlier that states:
r: devel

which did install R-devel (line 370
<https://travis-ci.org/kevinrue/TVTB/builds/169258984#L370> of the
previous
build):

$curl -Lo /tmp/R-devel.xz https://s3.amazonaws.com/
rstudio-travis/R-devel.xz

I honestly don't know how YAML instructions work on Travis, but maybe some
action must be taken before "bioc-devel" becomes synonym to "R-devel" ?

Thanks for your help.
Kevin


On Thu, Oct 20, 2016 at 4:49 PM, Lukas Weber <lukmweber at gmail.com> wrote:

Hi Kevin,

I have been using the following setup in my .travis.yml file. Travis CI
should automatically use the correct version of R for the Bioconductor
version specified in the "r: bioc-devel" line (you can replace this with
"r: bioc-release" to use the release version). There is some more
information here: https://docs.travis-ci.com/user/languages/r/ (see the
Bioconductor section).

language: r
r: bioc-devel
sudo: false
cache: packages
r_github_packages:
  - jimhester/covr
after_success:
  - Rscript -e 'covr::codecov()'

The additional "covr" lines are for checking unit test code coverage with
codecov.

Lukas


On Thu, Oct 20, 2016 at 4:51 PM, Kevin RUE <kevinrue67 at gmail.com> wrote:

Actually, nevermind, I think I solved the issue of R-devel with the
following YAML instructions:

language: r
r: devel

before_install:
    - Rscript -e 'source(file = "http://bioconductor.org/biocLite.R
");tryCatch(useDevel(devel = TRUE), error =

function(err){message(err)})'

    - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then tlmgr install bera
nowidow parnotes marginfix; fi

Now the build <https://travis-ci.org/kevinrue/TVTB/builds/169246652>

only

fails because S4Vectors is not available on the new devel branch, but

I'm

sure that's going to resolve itself within the next couple of

builds/days.

All the best,
Kevin


Just for the record, prior to the recent BioC release, I had the

following

(working) configuration. I have never been sure how elegant that was (I
may
have combined some redundant bioc instructions):

language: r
use_bioc: true
bioc_required: true
r: bioc-release
before_install:
    - Rscript -e 'source(file = "http://bioconductor.org/biocLite.R
");tryCatch(useDevel(devel = TRUE), error =

function(err){message(err)})'

    - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then tlmgr install bera
nowidow parnotes marginfix; fi



On Thu, Oct 20, 2016 at 1:31 PM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

Sorry, can you try one more time? Thanks, Martin


On 10/20/2016 06:06 AM, Rodriguez Martinez, Andrea wrote:

Thanks for your reply.


I have successfully removed BiocInstaller by hand, restart R, and

then,

installed with:


source("https://bioconductor.org/biocLite.R")

Warning in install.packages :
  URL
'https://bioconductor.org/packages/3.4/bioc/bin/macosx/maver
icks/contrib/3.4/PACKAGES.gz':
status was '404 Not Found'
Warning in install.packages :
  URL
'https://bioconductor.org/packages/3.4/bioc/bin/macosx/maver
icks/contrib/3.4/PACKAGES':
status was '404 Not Found'
Warning in install.packages :
  unable to access index for repository
https://bioconductor.org/packages/3.4/bioc/bin/macosx/maveri
cks/contrib/3.4:
  cannot download all files
installing the source package ?BiocInstaller?

trying URL
'https://bioconductor.org/packages/3.4/bioc/src/contrib/Bioc
Installer_1.24.0.tar.gz'
Content type 'application/x-gzip' length 17756 bytes (17 KB)
==================================================
downloaded 17 KB

* installing *source* package ?BiocInstaller? ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
Warning: Bioconductor version 3.4 is too old for R version 3.4.0; see
  https://bioconductor.org/install/#troubleshoot-biocinstaller
* DONE (BiocInstaller)

The downloaded source packages are in
?/private/var/folders/z8/8jwlrtqx3270h05ncg1xwzs80000gn/T/
RtmpRmVsc5/downloaded_packages?
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help

BiocInstaller::useDevel()

Error: 'devel' version requires a more recent R

Thanks very much,

Andrea



------------------------------------------------------------

------------

*From:* Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of
Martin Morgan <martin.morgan at roswellpark.org>
*Sent:* 20 October 2016 10:28:34
*To:* Michael Lawrence; bioc-devel at r-project.org
*Subject:* Re: [Bioc-devel] Fwd: BiocInstaller::useDevel() Error:

'devel' version requires a more recent R

On 10/20/2016 12:00 AM, Michael Lawrence wrote:

---------- Forwarded message ----------
From: Rodriguez Martinez, Andrea <andrea.rodriguez-martinez13 at i
mperial.ac.uk>
Date: Wed, Oct 19, 2016 at 3:33 PM
Subject: Re: [Bioc-devel] BiocInstaller::useDevel() Error: 'devel'
version requires a more recent R
To: Michael Lawrence <lawrence.michael at gene.com>


Sorry again,

I have just installed the R-devel version and now I get the

following

error: "Bioconductor does not yet support R version 3.4.0"

Thank you, you installed BiocInstaller in R-devel (R-3.4) before
Bioconductor officially supported R-3.4, and need to manually remove

and

re-install BiocInstaller.

I have updated the online configure, so in a new session, try to load
the BiocInstaller package and you should now see

Bioconductor version 3.4 is too old for R version 3.4.0; see
   https://bioconductor.org/install/#troubleshoot-biocinstaller

The instructions are to remove BiocInstaller by hand

   remove.packages("BiocInstaller")
   remove.packages("BiocInstaller") # fails, if not then investigate

and install again

   source("https://bioconductor.org/biocLite.R")

Martin

Thanks,

Andrea

message

(using R.3.3.1)


BiocInstaller::useDevel()

Error: 'devel' version requires a more recent R

Any help with this?

Thanks very much in advance,

Andrea

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